EMIFile

class seremi.EMIFile(path: str | Path)

Bases: object

Read an EMI file, which contains detailed metadata and the last frame of an SER.

close()

Close internal resource handles

domain: str

domain metadata field

img_height: int

height of the image in pixels

img_width: int

width of the image in pixels

info_dict: dict

metadata XML object converted to dictionary

open()

Open the EMI and populate metadata fields. This method does not read frame contents.

original_filepath: str

the filepath of the SER when it was saved the first time

path: Path

user-provided path

read_frame() → ndarray

Extract the one frame stored inside the EMI file. In my testing, this image is always the last frame of the corresponding SER file. :return: 2D int32 array

class seremi.SERFile(path: Path | str)

Bases: object

Read a SER microscope image file, which contains multiple frames. Initially, on opening an SER file, only metadata is read. To access image content of a particular frame, call read_frame().

SER files contain very little metadata. Instead, for a SER file “abc_1.ser”, there exists a corresponding EMI file “abc.emi”, which contains detailed metadata corresponding to the SER.

close()

Close internal resource handles

img_height: int

height of each image in pixels

img_width: int

width of each image in pixels

num_frames: int

number of images inside this one SER file

open()

Open the SER file and populate metadata fields. This method does not read frame contents.

path: Path

user-provided path of the image file

read_all_frames() → list[ndarray]

Extract the content of all the frames. :return: list of 2D int32 arrays

read_frame(idx: int) → ndarray

Extract the content of one of the images inside this SER file. :param idx: 0-indexed frame number :return: 2D int32 array

read_last_frame() → ndarray

Extract the content of the last frame. :return: 2D int32 array

read_timestamp(idx: int) → int

Read UNIX timestamp saved inside this file. :return: integer seconds since Jan 1, 1970, UTC.